RetrogeneDB ID: retro_ocun_437

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 10:31074989..31076516(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSOCUG00000000464
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DLD
• Ensembl ID: ENSOCUG00000014667
• Aliases: None
• Description: dihydrolipoamide dehydrogenase [Source:HGNC Symbol;Acc:2898]

Sequence

>retro_ocun_437
ATGCAGAGCTGGAGTCGTGTGTACTGCTCCTTGGCCAAGAGAGGCCATTTCAATCGAATATCTCATGGCCTACAGGGAGT
TTCTGTAGTGCCCCCTGAGAACTTACGCAGATCAATCCATTGATGCTGATGTGACTGTGATAGGTTCTGGTCCTGGAGGA
TATGTTGCTGCTATTAAAGCTGCCCAGTTAGGCTTTAAGACAGTCTGCGTTGAGAAAAATGAGATGCTTGGAGGGACATG
CTTGAATGTGGGCTGTATTCCTTCTAAGGCTTTATCGAATAACTCTCATTATTACCATATGGCCCATGGAAAAGATTTTG
CATCTAGGGGAATTGAAATGTCTGAAGTTCGCTTGAATTTAGAGAAGATGATGGAGCAGAAGAGTACTGCAGTTAAAGCT
TTAACAGGTGGAATTGCCCATTTATTCAAACAGAATAAGGTTGTTCATGTCAATGGATATGGAAAGATTACTGGCAAAAA
TCAGGTCACTGCTACAAAAGCTGATGGCAGCACGCAGGTCATCGACACAAAGAATATTCTTGTAGCTACAGGATCAGAAG
TTACTCCTTTTCCTGGAATCACGATTGATGAAGATACAATAGTATCATCTACAGGTGCTTTATCTTTAAAAAAAGTTCCA
GAAAAGATGGTTGTTATTGGTGCAGGAGTAATAGGAGTAGAATTGGGTTCAGTGTGGCAAAGACTTGGTGCAGACGTGAC
AGCAGTTGAATTTTTGGGTCATGTAGGTGGAGTTGGAATTGACATGGAGATATCTAAAAACTTTCAACGCATCCTTCAAA
AACAAGGATTTAAATTTAAATTGAATACAAAGGTTACTGGTGCTACCAAGAAGCCAGATGGCAAAATTGATGTGTCTATT
GAAGCTGCTTCTGGTGGTAAAGCGGAAGTCATCACTTGCGACGTGCTCTTGGTTTGCATTGGGCGAGACCCTTTACTCAG
AATTTGGGACTGGAAGAGCTTGGGATTGAACTAGATCCCAGAGGCAGAATCCCAGTCAATACCAGATTCCAAACTAAGAT
TCCAAACATCTATGCTATTGGTGATGTGGTTGCTGGCCCGATGCTGGCTCACAAAGCAGAAGATGAGGGCATCCTCTGTG
TCGAAGGAATGGCTGGTGGCGCAGTGCACATTGATTACAACTGCGTGCCGTCCGTGATTTACACGCACCCTGAGGTGGCT
TGGGTTGGAAAATCGGAAGAGCAGTTGAAGGAAGAGGGTATTGAGTACAAAGTTGGTAAGTTCCCGTTTGCTGCCAACAG
CAGAGCTAAGACTAATGCTGACACAGACGGCATGGTGAAGATTCTCGGGCAGAAGTCGACAGACAGAGTACTGGGAGCAC
ATATTCTAGGACCAGGTGCTGGAGAAATGGTGAATGAAGCGGCTCTGGCTTTGGAATACGGGGCATCCTGTGAAAATATA
GCTAGAGTCTGTCGCGCGCATCCGACCTTATCAGAAGCTTTCAGAGAAGCAAACCTGGCTGCATCATTTGGCAAATCAAT
CAACTTT

Alignment

ORF - retro_ocun_437 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQSWSRVYCSLAKRGHFNRISHGIQGVSVVP-LRTYADQSIDADVTVIGSGPGGYVAAIKAAQLGFKTVC
          MQSWSRVYCSLAKRGHFNRISHG.QGVSVVP.LRTYADQSIDADVTVIGSGPGGYVAAIKAAQLGFKTVC
Retrocopy MQSWSRVYCSLAKRGHFNRISHGLQGVSVVP>LRTYADQSIDADVTVIGSGPGGYVAAIKAAQLGFKTVC

Parental  VEKNETLGGTCLNVGCIPSKALLNNSHYYHMAHGKDFASRGIEMSEVRLNLEKMMEQKSTAVKALTGGIA
          VEKNE.LGGTCLNVGCIPSKAL.NNSHYYHMAHGKDFASRGIEMSEVRLNLEKMMEQKSTAVKALTGGIA
Retrocopy VEKNEMLGGTCLNVGCIPSKALSNNSHYYHMAHGKDFASRGIEMSEVRLNLEKMMEQKSTAVKALTGGIA

Parental  HLFKQNKVFHRYNFKLLTSTNQVTATKADGSTQVIDT-NILVATGSEVTPFPGITIDEDTIVSSTGALSL
          HLFKQNKV.H.......T..NQVTATKADGSTQVIDT.NILVATGSEVTPFPGITIDEDTIVSSTGALSL
Retrocopy HLFKQNKVVHVNGYGKITGKNQVTATKADGSTQVIDTKNILVATGSEVTPFPGITIDEDTIVSSTGALSL

Parental  KKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVT
          KKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVT
Retrocopy KKVPEKMVVIGAGVIGVELGSVWQRLGADVTAVEFLGHVGGVGIDMEISKNFQRILQKQGFKFKLNTKVT

Parental  GATKKPDGKIDVSIEAASGGKAEVITCDVLLVCIGR-RPFTQNLGLEELGIELDPRGRIPVNTRFQTKIP
          GATKKPDGKIDVSIEAASGGKAEVITCDVLLVCIGR.RPFTQNLGLEELGIELDPRGRIPVNTRFQTKIP
Retrocopy GATKKPDGKIDVSIEAASGGKAEVITCDVLLVCIGR<RPFTQNLGLEELGIELDPRGRIPVNTRFQTKIP

Parental  NIYAIGDVVAGPMLAHKAEDEGILCVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKV
          NIYAIGDVVAGPMLAHKAEDEGILCVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKV
Retrocopy NIYAIGDVVAGPMLAHKAEDEGILCVEGMAGGAVHIDYNCVPSVIYTHPEVAWVGKSEEQLKEEGIEYKV

Parental  GKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCEDIARVCHAHP
          GKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCE.IARVC.AHP
Retrocopy GKFPFAANSRAKTNADTDGMVKILGQKSTDRVLGAHILGPGAGEMVNEAALALEYGASCENIARVCRAHP

Parental  TLSEAFREANLAASFGKSINF
          TLSEAFREANLAASFGKSINF
Retrocopy TLSEAFREANLAASFGKSINF

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	12.36 RPM	70.14 RPM
SRP017611_kidney	15.81 RPM	88.08 RPM
SRP017611_liver	6.09 RPM	27.82 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_437 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_437 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_437 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000005312	1 retrocopy	retro_cpor_685,
Monodelphis domestica	ENSMODG00000016316	2 retrocopies	retro_mdom_1455, retro_mdom_448,
Oryctolagus cuniculus	ENSOCUG00000014667	1 retrocopy	retro_ocun_437 ,
Ictidomys tridecemlineatus	ENSSTOG00000007445	1 retrocopy	retro_itri_1226,
Tursiops truncatus	ENSTTRG00000003989	1 retrocopy	retro_ttru_699,